A key advantage of amino-modified SiO2 nanoparticles for delivery of phosphorylated nucleosides is a broad possibility for functionalization. It can be modified with ligands currently investigated in targeted drug delivery. To improve the efficacy for intracellular delivery, SiO2 nanoparticles were functionalized with tumor-targeting ligands folic acid, biotin or 5-fluorouracil. Studies of accumulation of these conjugates in HCT116 colon carcinoma cells revealed that the uptake of modified conjugates was significantly bigger compared to unmodified nanoparticles, with the biotinylated conjugate as the preferred compound. The nanocomposites of biotin modified SiO2 and 2′,3′-dideoxyuridine triphosphate showed a pronounced antiproliferative potency relative to the unmodified nanocomposites. Thus, multi-functionalization of SiO2 nanoparticle based conjugates has a major potential for delivery of nucleoside triphosphate analogues, therefore tentatively enhancing their bioactivity.